RNAseq analysis of CRISPR/Cas9-based perturbation of DNMT1 in FXS induced pluripotent stem cells

The primary mechanism causing Fragile X syndrome (FXS) is the expansion and silencing of a repetitive CGG sequence in the 5’-UTR of the FMR1 gene. Previous work has demonstrated that chemical disruption of DNA methylation induces FMR1 expression in FXS-iPSCs. To further explore the maintenance of DNA methylation in the FMR1 locus, and to test the possibility of FMR1 reactivation using gene targeting of a single epigenetic factor, we performed a global transcriptional analysis of FXS-iPSCs infected with a lentiviral construct containing Cas9 and sgRNA targeting DNMT1. To overcome the sensitivity of human PSCs to the loss of DNMT1, we infected FXS-iPSCs with a lentiviral vector containing sgRNA targeting DNMT1 and collected the culture 7-14 days following the initiation of selection.